Michael Flynn resigned as national security adviser because of his contacts with the Russian ambassador to Washington and his subsequent attempts to cover up the true nature of those contacts.

But his resignation is unlikely to mark the end of the Trump administration’s crisis of legitimacy over its relationship with Moscow. The manner of this matter suggests that this is only the beginning.

Flynn is the third Trump acolyte forced out over the question of links to the Russian government of Vladimir Putin. Paul Manafort, the former campaign manager, and Carter Page, a businessman Trump described as an adviser, both left last summer after reports surfaced about their contacts with the Kremlin.

The question of the true nature of the relationship between the president and Putin – who Trump once claimed to have met and later denied knowing – hung over his campaign and now looms over his presidency.

Many administrations have rocky starts, but there has never been a case of a national security adviser being forced to leave in less than a month. It has broken through the aura of impunity around the Trump White House and emboldened critics in their demands to know what the president knew and when he knew it.

“Trump may think Flynn is the sacrificial lamb, but the reality is that he is the first domino. To the extent the administration believes Flynn’s resignation will make the Russia story go away, they are mistaken,” said Susan Hennessey, a former NSA lawyer.

“Flynn’s resignation validates the suspicions of many in Washington that something is seriously amiss with regard to President Trump’s ties to Russia. This is the third member of Trump’s circle to be pushed out over Russia-linked scandals,” she said.

“This is only going to increase pressure from both the public and Congress demanding a full accounting of the nature of Trump’s connections to Russia both now and during the campaign.”

Donald Trump had 'full confidence' in Mike Flynn – hours later he was gone

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Trump clearly fought to keep his national security adviser in place, confident in his control of the executive branch and the grip of Republican loyalists on Congress.

The Washington Post reported on Monday that former acting attorney general Sally Yates informed him last month that Flynn’s misleading statements to Vice-President Mike Pence and other officials could leave him open to Russian blackmail. But it was Yates who was sacked, over her refusal to defend Trump’s travel ban, not Flynn.

The US intelligence agencies struck back, however, through an ever greater flow of leaks to the press, until Flynn’s position was untenable. The same leaks also suggest that the foundations of the whole administration are shaky.

Intelligence officials were quoted as saying that Flynn’s communications with the Russian ambassador to Washington, Sergei Kislyak, dated back to before the election, adding to the pile of unanswered questions about possible collusion between the Trump campaign and an operation, run by Vladimir Putin himself according to US intelligence agencies, to steer the US presidential election in Trump’s favour.

Flynn fell because he appears to have talked to Kislyak about measures the Obama administration was about to impose on Moscow at the end of December, including the expulsion of FSB intelligence officers, in retaliation for the interference in the election. According to the reports, he gave the impression that the sanctions would not last long, with the Trump administration less than three weeks from office.

Putin’s muted response took the Obama White House by surprise. He did not carry out tit-for-tat expulsions, but made a point of inviting the children of US diplomats in Moscow to the Kremlin for Christmas parties. Trump showed his approval in a 30 December tweet saying: “Great move on delay (by V. Putin) - I always knew he was very smart!”

Michael McFaul, a former US ambassador to Moscow, said: “This tweet does kind of make one wonder if the president-elect knew about the contents of Flynn conversation on sanctions with Kislyak.”

Numerous reports suggest that Trump did indeed intend to lift sanctions on Moscow and that executive orders were drafted to that effect in his first week in the White House, only to be deferred after protests from congressional Republicans, who have since started work on legislation that would take control over such sanctions out of the president’s hands. Theresa May also signaled her government’s determination that the sanctions should stay when she visited Washington.

But despite such concerted resistance from natural allies, Trump has persevered in defending Putin. When ultra-conservative talkshow host Bill O’Reilly suggested to Trump that Putin was “a killer”, the president replied: “There are a lot of killers. You think our country’s so innocent?”

They said could not corroborate the suggestion in the Steele reports that Russian intelligence had personally compromising material on Trump from his behaviour on trips to Russia, but that they had independent evidence of contacts between individuals in Trump’s entourage and Russian officials.

The Foreign Intelligence Surveillance Act (Fisa) court is reported to have granted a wiretap warrant in mid-October to allow the justice department’s national security division to look into contacts between two Russian banks and Trump associates.

Those investigations appear to be continuing but within the hostile environment of an executive controlled from the Trump White House. However, intelligence officials have now signalled that they are prepared to leak aggressively if they feel they are being muzzled.

Ultimately, the fundamental questions about Trump’s links with Russia may only be answered in Congress. The Senate intelligence, armed services and foreign relations committees, as well as the House intelligence committee, have all voiced intentions to look into the allegations, and subpoena top officials if necessary. But so far those enquiries have not properly got off the ground in the face of Republican reluctance to maim an executive that is fast-tracking much of the party’s social, economic and fiscal agenda.

If the leaks continue at their present rate, however, it is possible than congressional Republicans will flip, and decide that Trump is more of a liability than an asset. That moment has not been reached yet, but the fall of Flynn has brought it closer.